About 46,000 hectares (113,666 acres) of fields in South Phyongan and South Hwanghae provinces were decimated, KCNA said.
It added that those areas were the "main granaries of the country."
"Unprecedented torrential rains have poured down in the DPRK [Democratic People's Republic of Korea] for days in succession from Aug 7, throwing a shadow over [the] prospect of the agricultural production," the agency said.
Even with a good harvest, North Korea still falls about one million tonnes short of the food it needs to feed its 23 million people, reports have said.
The North's state media said the storms that battered wide swaths of the country left "hundreds" dead or missing.
|Parts of the country remain underwater|
To cope with the damage, the North has mobilised the military to help with recovery efforts, South Korea's Yonhap news agency reported.
The UN World Food Program said that North Korean officials reported 200,000-300,000 people were now homeless, with the total number of those affected probably much larger.
Paul Risley, Asia spokesman for the UN World Food Programme, said a UN assessment team has visited one flood-hit area near Pyongyang, and added that North Korea was seeking international help.
"There was great concern that because these floods occurred during the period of pollination, that it is likely that these floods will have a very significant impact on the quantity of harvest," Risley said.
But because of the floods, aid is expected to be diverted and the WFP will likely launch a new international appeal for assistance, Risley said.
Bad weather risk
The WFP is able to produce critical food items such as biscuits from factories that it runs inside North Korea.
However, it still needs outside commodities like wheat and rice to make them that are shipped via roads and rail.
In New York on Tuesday, Ban Ki-moon, the UN Secretary-General promised during a meeting with Pak Gil Yon, the North Korean ambassador that the world body would do all it could to help.
The South Korean government has said it was ready to aid its neighbour, but has yet to receive a request.
The US said it was also considering offering aid.
The North is especially susceptible to bad weather because of a vicious circle where people strip hillsides of natural vegetation to create more arable land to grow food - increasing the risk of floods.
Residents have used every scrap of wood from the countryside to cook food or heat homes through the bitter winters, leaving large areas of the country vulnerable to flooding and landslides.